NM_000527.5(LDLR):c.1009G>A (p.Glu337Lys) AND Cardiovascular phenotype

Germline classification:: Likely benign (1 submission)
Last evaluated:: Oct 27, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002438614.2

Allele description [Variation Report for NM_000527.5(LDLR):c.1009G>A (p.Glu337Lys)]

NM_000527.5(LDLR):c.1009G>A (p.Glu337Lys)

Gene:

LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.2

Genomic location:

Preferred name:

NM_000527.5(LDLR):c.1009G>A (p.Glu337Lys)

HGVS:

NC_000019.10:g.11110720G>A
NG_009060.1:g.26340G>A
NM_000527.5:c.1009G>AMANE SELECT
NM_001195798.2:c.1009G>A
NM_001195799.2:c.886G>A
NM_001195800.2:c.505G>A
NM_001195803.2:c.628G>A
NP_000518.1:p.Glu337Lys
NP_000518.1:p.Glu337Lys
NP_001182727.1:p.Glu337Lys
NP_001182728.1:p.Glu296Lys
NP_001182729.1:p.Glu169Lys
NP_001182732.1:p.Glu210Lys
LRG_274t1:c.1009G>A
LRG_274:g.26340G>A
LRG_274p1:p.Glu337Lys
NC_000019.9:g.11221396G>A
NM_000527.4:c.1009G>A

Protein change:

E169K

Links:

dbSNP: rs539080792

NCBI 1000 Genomes Browser:

rs539080792

Molecular consequence:

NM_000527.5:c.1009G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001195798.2:c.1009G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001195799.2:c.886G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001195800.2:c.505G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001195803.2:c.628G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cardiovascular phenotype
Identifiers:: MedGen: CN230736

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002741500	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Oct 27, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 28964736, 29353225, 33418990, 34834584 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002741500

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Oct 27, 2022)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Efficacy of alirocumab in 1191 patients with a wide spectrum of mutations in genes causative for familial hypercholesterolemia.

Defesche JC, Stefanutti C, Langslet G, Hopkins PN, Seiz W, Baccara-Dinet MT, Hamon SC, Banerjee P, Kastelein JJP.

J Clin Lipidol. 2017 Nov - Dec;11(6):1338-1346.e7. doi: 10.1016/j.jacl.2017.08.016. Epub 2017 Sep 4. Erratum in: J Clin Lipidol. 2020 Sep - Oct;14(5):742. doi: 10.1016/j.jacl.2020.09.010.

PubMed [citation]

PMID:: 28964736

Spectrum of mutations in index patients with familial hypercholesterolemia in Singapore: Single center study.

Pek SLT, Dissanayake S, Fong JCW, Lin MX, Chan EZL, Tang JI, Lee CW, Ong HY, Sum CF, Lim SC, Tavintharan S.

Atherosclerosis. 2018 Feb;269:106-116. doi: 10.1016/j.atherosclerosis.2017.12.028. Epub 2017 Dec 27.

PubMed [citation]

PMID:: 29353225

See all PubMed Citations (4)

Details of each submission

From Ambry Genetics, SCV002741500.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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